Pre-visualization of the normalized count data before any differential analysis
Warning message in is.na(x[[i]]): “is.na() applied to non-(list or vector) of type 'environment'”Warning message in rsqlite_fetch(res@ptr, n = n): “Don't need to call dbFetch() for statements, only for queries”
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
| GF_104w_F_1_2 | GF_104w_F_2_2 | GF_104w_F_3_2 | GF_104w_M_1_2 | GF_104w_M_2_2 | GF_52w_M_1_2 | GF_52w_M_2_2 | GF_52w_M_3_2 | GF_52w_M_4_2 | GF_8w_M_1_2 | ⋯ | SPF_104w_M_14_2 | SPF_8w_F_1_2 | SPF_8w_F_3_2 | SPF_8w_F_4_2 | SPF_8w_F_5_2 | GF_8w_F_1_2 | GF_8w_F_2_2 | GF_8w_F_3_2 | GF_8w_F_4_2 | GF_8w_F_5_2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610005C13Rik | 0.0000 | 0.00000 | 0.0000 | 1.768593 | 1.259244 | 0.8418979 | 4.942785 | 5.603216 | 7.231584 | 8.47277 | ⋯ | 5.28524 | 3.500355 | 2.112002 | 2.602398 | 0.00000 | 18.24998 | 0.00000 | 2.025447 | 5.268672 | 0.00000 |
| 0610007P14Rik | 868.4015 | 749.64927 | 910.3535 | 886.064952 | 992.913601 | 508.5063502 | 530.855142 | 514.375197 | 738.344705 | 603.98749 | ⋯ | 692.36648 | 763.077332 | 744.480801 | 908.237050 | 957.79030 | 898.54336 | 682.26034 | 612.697796 | 593.252445 | 809.27852 |
| 0610009B22Rik | 1021.3276 | 1169.19730 | 1180.9991 | 1224.750457 | 1558.313990 | 1038.9020466 | 876.850113 | 1016.423320 | 877.914273 | 948.95029 | ⋯ | 1206.79653 | 1268.295198 | 1164.769254 | 1295.994415 | 1446.89758 | 1040.24912 | 1020.67017 | 1142.352254 | 959.952003 | 1094.00091 |
| 0610009L18Rik | 28.2185 | 36.20465 | 18.2253 | 20.338816 | 38.406931 | 31.9921214 | 26.691041 | 22.412863 | 4.338950 | 61.73018 | ⋯ | 45.80542 | 42.004257 | 45.408049 | 102.794738 | 72.02239 | 48.30878 | 19.58642 | 11.139960 | 45.310578 | 24.36813 |
| 0610009O20Rik | 217.5555 | 278.98879 | 266.0893 | 226.379868 | 271.996624 | 299.7156634 | 349.949200 | 395.587025 | 309.511786 | 360.69794 | ⋯ | 178.81730 | 274.194454 | 252.384272 | 227.709862 | 184.89330 | 231.88216 | 158.86764 | 271.409933 | 304.529230 | 269.33199 |
| 0610010B08Rik | 0.0000 | 0.00000 | 0.0000 | 0.000000 | 0.000000 | 0.0000000 | 0.000000 | 0.000000 | 0.000000 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.000000 | 0.000000 | 0.00000 | 0.00000 | 0.00000 | 0.000000 | 0.000000 | 0.00000 |
Updating HTML index of packages in '.Library' Making 'packages.html' ... done
| Sepal.Length | Sepal.Width | Petal.Length | Petal.Width | Species |
|---|---|---|---|---|
| 5.1 | 3.5 | 1.4 | 0.2 | setosa |
| 4.9 | 3.0 | 1.4 | 0.2 | setosa |
| 4.7 | 3.2 | 1.3 | 0.2 | setosa |
| 4.6 | 3.1 | 1.5 | 0.2 | setosa |
| 5.0 | 3.6 | 1.4 | 0.2 | setosa |
| 5.4 | 3.9 | 1.7 | 0.4 | setosa |
'data.frame': 150 obs. of 5 variables: $ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ... $ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ... $ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ... $ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ... $ Species : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...
pickSoftThreshold: will use block size 4378. pickSoftThreshold: calculating connectivity for given powers... ..working on genes 1 through 4378 of 10219 ..working on genes 4379 through 8756 of 10219 ..working on genes 8757 through 10219 of 10219 Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. 1 2 0.144 -0.617 0.901 644.0000 6.20e+02 1390.00 2 4 0.691 -1.460 0.964 114.0000 9.21e+01 438.00 3 6 0.783 -1.840 0.970 31.1000 1.94e+01 198.00 4 8 0.790 -2.020 0.962 11.0000 5.03e+00 106.00 5 10 0.832 -1.990 0.985 4.6100 1.49e+00 63.10 6 12 0.851 -1.960 0.988 2.1900 4.90e-01 40.10 7 14 0.876 -1.890 0.988 1.1500 1.72e-01 26.70 8 16 0.886 -1.820 0.971 0.6430 6.43e-02 18.40 9 18 0.899 -1.780 0.970 0.3830 2.50e-02 13.60 10 20 0.882 -1.770 0.946 0.2400 1.02e-02 10.40 11 22 0.917 -1.720 0.984 0.1560 4.29e-03 8.11 12 24 0.902 -1.700 0.962 0.1050 1.86e-03 6.46 13 26 0.408 -2.230 0.416 0.0724 8.32e-04 5.23 14 28 0.416 -2.190 0.427 0.0514 3.76e-04 4.28 15 30 0.931 -1.630 0.984 0.0372 1.74e-04 3.55
Parameters for network construction
ERROR while rich displaying an object: Error in sprintf(wrap, header, body): 'fmt' length exceeds maximal format length 8192
Traceback:
1. FUN(X[[i]], ...)
2. tryCatch(withCallingHandlers({
. rpr <- mime2repr[[mime]](obj)
. if (is.null(rpr))
. return(NULL)
. prepare_content(is.raw(rpr), rpr)
. }, error = error_handler), error = outer_handler)
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. doTryCatch(return(expr), name, parentenv, handler)
6. withCallingHandlers({
. rpr <- mime2repr[[mime]](obj)
. if (is.null(rpr))
. return(NULL)
. prepare_content(is.raw(rpr), rpr)
. }, error = error_handler)
7. mime2repr[[mime]](obj)
8. repr_latex.matrix(obj)
9. repr_matrix_generic(obj, sprintf("\\begin{tabular}{%s}\n%%s%%s\\end{tabular}\n",
. cols), "%s\\\\\n\\hline\n", " &", " %s &", "%s", "\t%s\\\\\n",
. "%s &", " %s &", escape_fun = latex_escape_vec, ...)
10. sprintf(wrap, header, body)
| 0610007P14Rik | 0610009B22Rik | 0610009L18Rik | 0610009O20Rik | 0610010F05Rik | 0610010K14Rik | Mettl26 | 0610012G03Rik | 0610030E20Rik | 0610037L13Rik | ⋯ | Zw10 | Zwint | Zxda | Zxdb | Zxdc | Zyg11b | Zyx | Zzef1 | Zzz3 | Hikeshi | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GF_104w_F_1_2 | 868.4015 | 1021.328 | 28.21850 | 217.5555 | 411.4439 | 1351.757 | 283.0953 | 693.6289 | 899.3508 | 449.6754 | ⋯ | 618.0761 | 1471.913 | 297.6596 | 130.1692 | 923.9282 | 1333.552 | 2864.633 | 396.8795 | 752.7967 | 668.1412 |
| GF_104w_F_2_2 | 749.6493 | 1169.197 | 36.20465 | 278.9888 | 461.0769 | 1516.336 | 207.6443 | 686.8236 | 759.2329 | 526.0323 | ⋯ | 797.5672 | 1539.763 | 243.8490 | 198.0607 | 981.7850 | 1340.637 | 3358.514 | 364.1762 | 597.3768 | 703.8610 |
| GF_104w_F_3_2 | 910.3535 | 1180.999 | 18.22530 | 266.0893 | 288.8709 | 1852.601 | 222.3486 | 868.4353 | 540.3800 | 444.6972 | ⋯ | 731.7456 | 1375.099 | 153.0925 | 171.3178 | 922.1999 | 1181.910 | 3058.205 | 209.5909 | 644.2642 | 770.9300 |
| GF_104w_M_1_2 | 886.0650 | 1224.750 | 20.33882 | 226.3799 | 278.5534 | 1551.056 | 190.1237 | 823.2799 | 525.2720 | 607.5116 | ⋯ | 466.9085 | 1752.675 | 172.4378 | 344.8756 | 683.5611 | 1295.494 | 2789.955 | 261.7517 | 944.4285 | 687.9826 |
| GF_104w_M_2_2 | 992.9136 | 1558.314 | 38.40693 | 271.9966 | 304.1073 | 1911.532 | 243.0340 | 778.8422 | 707.6949 | 586.8075 | ⋯ | 878.3224 | 1957.494 | 147.9611 | 249.3302 | 1003.6172 | 1205.726 | 2819.446 | 200.8494 | 785.1384 | 583.6594 |
| GF_52w_M_1_2 | 508.5064 | 1038.902 | 31.99212 | 299.7157 | 392.3244 | 1173.606 | 182.6919 | 589.3286 | 1047.3210 | 621.3207 | ⋯ | 768.6528 | 1397.551 | 287.9291 | 275.3006 | 924.4039 | 1674.535 | 2206.614 | 749.2892 | 1163.5029 | 493.3522 |
Calculating module eigengenes block-wise from all genes
Flagging genes and samples with too many missing values...
..step 1
....pre-clustering genes to determine blocks..
Projective K-means:
..k-means clustering..
..merging smaller clusters...
Block sizes:
gBlocks
1 2 3
4997 4015 1207
..Working on block 1 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 1 into file norm_genes_TOM-block.1.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..Working on block 2 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 2 into file norm_genes_TOM-block.2.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..Working on block 3 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 3 into file norm_genes_TOM-block.3.RData
....clustering..
....detecting modules..
No modules detected in block 3
..reassigning 1 genes from module 1 to modules with higher KME.
..reassigning 1 genes from module 9 to modules with higher KME.
..reassigning 3 genes from module 10 to modules with higher KME.
..reassigning 3 genes from module 11 to modules with higher KME.
..reassigning 1 genes from module 14 to modules with higher KME.
..merging modules that are too close..
mergeCloseModules: Merging modules whose distance is less than 0.2
Calculating new MEs...
0 1 2 3 4 5 6 7 8 9 10 11 8786 446 260 191 95 93 86 62 56 53 49 42
TOM calculation: adjacency.. ..will use 4 parallel threads. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done.
| 0610030E20Rik | 1600020E01Rik | Zfp974 | 1700094D03Rik | 1700112E06Rik | 1810026B05Rik | Ndufaf8 | 2010107E04Rik | 2210016L21Rik | 2310033P09Rik | ⋯ | Zmpste24 | Zmym6 | Znhit2 | Znrd1 | Znrf1 | Znrf2 | Zrsr2 | Zscan26 | Zswim8 | Zzef1 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610030E20Rik | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| 1600020E01Rik | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 |
| Zfp974 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1700094D03Rik | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| 1700112E06Rik | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1810026B05Rik | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 |
[1] 1
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
3121 GO:0006325 1.535024e-17 1 59
5998 GO:0016569 1.552323e-14 1 48
4834 GO:0010467 2.180602e-13 1 177
5999 GO:0016570 8.098099e-13 1 40
9705 GO:0034641 9.689717e-13 1 194
14200 GO:0051171 1.033361e-12 1 156
numInCat term ontology
3121 683 chromatin organization BP
5998 489 chromatin modification BP
4834 4726 gene expression BP
5999 384 histone modification BP
9705 5508 cellular nitrogen compound metabolic process BP
14200 3783 regulation of nitrogen compound metabolic process BP
[1] 2
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
9908 GO:0034976 3.637326e-08 1.0000000 16
3468 GO:0006810 1.089150e-07 1.0000000 94
5357 GO:0015031 1.267559e-07 1.0000000 50
14240 GO:0051234 3.386036e-07 1.0000000 95
12359 GO:0045184 6.817248e-07 0.9999997 52
13425 GO:0048193 9.479241e-07 0.9999998 14
numInCat term ontology
9908 204 response to endoplasmic reticulum stress BP
3468 4082 transport BP
5357 1649 protein transport BP
14240 4231 establishment of localization BP
12359 1809 establishment of protein localization BP
13425 186 Golgi vesicle transport BP
[1] 3
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
3468 GO:0006810 2.086915e-24 1 82
14240 GO:0051234 2.515869e-24 1 83
14206 GO:0051179 6.256614e-24 1 92
14955 GO:0055114 9.097327e-22 1 43
12773 GO:0046034 6.631370e-20 1 24
4467 GO:0009167 3.481026e-19 1 24
numInCat term ontology
3468 4082 transport BP
14240 4231 establishment of localization BP
14206 5342 localization BP
14955 883 oxidation-reduction process BP
12773 181 ATP metabolic process BP
4467 206 purine ribonucleoside monophosphate metabolic process BP
[1] 4
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 5
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 6
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 7
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
1052 GO:0002376 0 1 39
1090 GO:0002443 0 1 12
4626 GO:0009615 0 1 14
9407 GO:0034097 0 1 16
14463 GO:0051607 0 1 12
16706 GO:0071345 0 1 15
numInCat term ontology
1052 2158 immune system process BP
1090 290 leukocyte mediated immunity BP
4626 307 response to virus BP
9407 553 response to cytokine BP
14463 269 defense response to virus BP
16706 458 cellular response to cytokine stimulus BP
[1] 8
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
15 GO:0000028 0 1 7
936 GO:0002181 0 1 9
3177 GO:0006412 0 1 40
3251 GO:0006518 0 1 40
3465 GO:0006807 0 1 46
3974 GO:0008152 0 1 46
numInCat term ontology
15 19 ribosomal small subunit assembly BP
936 49 cytoplasmic translation BP
3177 597 translation BP
3251 738 peptide metabolic process BP
3465 5831 nitrogen compound metabolic process BP
3974 9868 metabolic process BP
[1] 9
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 10
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 11
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
14475 GO:0051641 4.691842e-07 0.9999999 17
9687 GO:0034613 4.023301e-06 0.9999994 13
16411 GO:0070727 4.372873e-06 0.9999993 13
3940 GO:0008104 5.268680e-06 0.9999990 16
12359 GO:0045184 7.691099e-06 0.9999987 14
14206 GO:0051179 1.682391e-05 0.9999959 24
numInCat term ontology
14475 2172 cellular localization BP
9687 1453 cellular protein localization BP
16411 1464 cellular macromolecule localization BP
3940 2291 protein localization BP
12359 1809 establishment of protein localization BP
14206 5342 localization BP
[1] "1: 12 - 2.69058295964126%" [1] "2: 14 - 5.38461538461539%" [1] "3: 6 - 3.1413612565445%" [1] "4: 1 - 1.05263157894737%" [1] "5: 1 - 1.0752688172043%" [1] "6: 4 - 4.65116279069767%" [1] "7: 2 - 3.2258064516129%" [1] "8: 2 - 3.57142857142857%" [1] "9: 2 - 3.77358490566038%" [1] "10: 0 - 0%" [1] "11: 0 - 0%"
Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : “EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : “number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : “EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : “number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : “EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : “number of items read is not a multiple of the number of columns”

Tree with all GOs at "../results/dge/global_GO_network.png"
| GO:0050896 | GO:0008092 | GO:0002376 | GO:0048731 | GO:0048856 | GO:0044707 | GO:0006952 | GO:0006950 | GO:0032502 | GO:0007275 | ⋯ | GO:0018586 | GO:0018588 | GO:0018589 | GO:0018590 | GO:0018591 | GO:0018592 | GO:0018593 | GO:0034751 | GO:0051286 | GO:0061303 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610009O20RIK | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| FMC1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1190002N15RIK | 1 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 1 | 1 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1600002K03RIK | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1600014C10RIK | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| ZFP974 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 0610009O20RIK | FMC1 | 1190002N15RIK | 1600002K03RIK | 1600014C10RIK | ZFP974 | 1810011O10RIK | NDUFAF8 | 2010107E04RIK | 2010107G23RIK | ⋯ | PALM | PLEKHB1 | RAB25 | RND2 | SFMBT2 | SLC29A2 | SLC4A10 | UBXN11 | XLR4A | ZFP599 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610009O20RIK | 0 | 19 | 21 | 5 | 9 | 11 | 32 | 9 | 9 | 0 | ⋯ | 27 | 15 | 19 | 21 | 19 | 9 | 12 | 14 | 11 | 11 |
| FMC1 | 19 | 0 | 15 | 5 | 9 | 9 | 20 | 9 | 9 | 0 | ⋯ | 20 | 14 | 14 | 14 | 18 | 9 | 8 | 11 | 10 | 9 |
| 1190002N15RIK | 21 | 15 | 0 | 8 | 11 | 4 | 38 | 9 | 11 | 2 | ⋯ | 37 | 25 | 32 | 31 | 14 | 12 | 18 | 8 | 15 | 4 |
| 1600002K03RIK | 5 | 5 | 8 | 0 | 8 | 0 | 5 | 5 | 8 | 3 | ⋯ | 7 | 8 | 7 | 6 | 4 | 7 | 5 | 5 | 4 | 0 |
| 1600014C10RIK | 9 | 9 | 11 | 8 | 0 | 0 | 9 | 9 | 12 | 3 | ⋯ | 11 | 12 | 8 | 10 | 8 | 11 | 5 | 7 | 8 | 0 |
| ZFP974 | 11 | 9 | 4 | 0 | 0 | 0 | 47 | 0 | 0 | 0 | ⋯ | 29 | 4 | 4 | 4 | 47 | 0 | 13 | 7 | 1 | 47 |
Module 1: chromatine/chromosome organization/RNA metabolic process
Module 2: response to endoplasmic reticulum stress/transport
Module 3: metabolic process (ATP, ribonucleoside)
Module 4
Module 5
Module 6: metabolic process (primary, cellular)
Module 7: immune system
Module 8: translation/rRNA
Module 9
Module 10: organelle
Module 11: localization